Cholesterol 7α-hydroxylase (CYP7A1) plays a crucial role in the synthesis of bile acid, fatty acid and cholesterol metabolism in human and rodent. However, a little was known in the literature on the question of the effect of CYP7A1 gene on poultry lipid homeostasis. This study was performed to investigate the effect of the polymorphisms of CYP7A1 gene on lipid traits in Tianzhu Black Muscovy (Cairina moschata). We detected two novel silent mutations, CDS 216 A>G and CDS 681 T>A in exon 2 and exon 3 of CYP7A1 gene, respectively, and both SNPs changed DNA single strand conformation. The A and T allele of CDS 216 A>G and CDS 681 T>A was dominant allele, and its frequency was 0.554 and 0.800, respectively. Each SNP resulted in three genotypes. The genotypic distribution of CDS 216 A>G and CDS 681 T>A was not deviated and deviated from Hardy-Weinberg equilibrium (HWE), respectively. The polymorphism information content (PIC) of CDS 216 A>G and CDS 681 T>A was 0.372 and 0.269, respectively, and both belonged to medium levels of genetic diversity. Association analysis revealed that two SNPs were significant association with at least four of seven lipid indexes. Allele A of CDS 216 A>G locus and allele T of CDS 681 T>A locus was favorable to improving meat quality, respectively. Three haplotypes and six diplotypes were identified by the combination of two SNPs. Diplotypes had dominantly affected on tested lipid indexes except for IMF. Diplotype H1H1 was advantageous for the improvement of meat quality. Therefore, our data suggested that two novel SNPs: CDS 216 A>G and CDS 681 T>A in CYP7A1 gene were potential candidate markers for improving meat quality. It also provides reference data for early breeding and selection of Tianzhu Black Muscovy.